391 research outputs found
Functional connectivity estimation over large networks at cellular resolution based on electrophysiological recordings and structural prior
Despite many structural and functional aspects of the brain organization have been extensively studied in neuroscience, we are still far from a clear understanding of the intricate structure-function interactions occurring in the multi-layered brain architecture, where billions of different neurons are involved. Although structure and function can individually convey a large amount of information, only a combined study of these two aspects can probably shade light on how brain circuits develop and operate at the cellular scale. Here, we propose a novel approach for refining functional connectivity estimates within neuronal networks using the structural connectivity as prior. This is done at the mesoscale, dealing with thousands of neurons while reaching, at the microscale, an unprecedented cellular resolution. The High-Density Micro Electrode Array (HD-MEA) technology, combined with fluorescence microscopy, offers the unique opportunity to acquire structural and functional data from large neuronal cultures approaching the granularity of the single cell. In this work, an advanced method based on probabilistic directional features and heat propagation is introduced to estimate the structural connectivity from the fluorescence image while functional connectivity graphs are obtained from the cross-correlation analysis of the spiking activity. Structural and functional information are then integrated by reweighting the functional connectivity graph based on the structural prior. Results show that the resulting functional connectivity estimates are more coherent with the network topology, as compared to standard measures purely based on cross-correlations and spatio-temporal filters. We finally use the obtained results to gain some insights on which features of the functional activity are more relevant to characterize actual neuronal interactions
Investigating Brain Functional Networks in a Riemannian Framework
The brain is a complex system of several interconnected components which can be categorized at different Spatio-temporal levels, evaluate the physical connections and the corresponding functionalities. To study brain connectivity at the macroscale, Magnetic Resonance Imaging (MRI) technique in all the different modalities has been exemplified to be an important tool. In particular, functional MRI (fMRI) enables to record the brain activity either at rest or in different conditions of cognitive task and assist in mapping the functional connectivity of the brain.
The information of brain functional connectivity extracted from fMRI images can be defined using a graph representation, i.e. a mathematical object consisting of nodes, the brain regions, and edges, the link between regions. With this representation, novel insights have emerged about understanding brain connectivity and providing evidence that the brain networks are not randomly linked. Indeed, the brain network represents a small-world structure, with several different properties of segregation and integration that are accountable for specific functions and mental conditions. Moreover, network analysis enables to recognize and analyze patterns of brain functional connectivity characterizing a group of subjects.
In recent decades, many developments have been made to understand the functioning of the human brain and many issues, related to the biological and the methodological perspective, are still need to be addressed. For example, sub-modular brain organization is still under debate, since it is necessary to understand how the brain is functionally organized. At the same time a comprehensive organization of functional connectivity is mostly unknown and also the dynamical reorganization of functional connectivity is appearing as a new frontier for analyzing brain dynamics. Moreover, the recognition of functional connectivity patterns in patients affected by mental disorders is still a challenging task, making plausible the development of new tools to solve them.
Indeed, in this dissertation, we proposed novel methodological approaches to answer some of these biological and neuroscientific questions. We have investigated methods for analyzing and detecting heritability in twin's task-induced functional connectivity profiles. in this approach we are proposing a geodesic metric-based method for the estimation of similarity between functional connectivity, taking into account the manifold related properties of symmetric and positive definite matrices.
Moreover, we also proposed a computational framework for classification and discrimination of brain connectivity graphs between healthy and pathological subjects affected by mental disorder, using geodesic metric-based clustering of brain graphs on manifold space. Within the same framework, we also propose an approach based on the dictionary learning method to encode the high dimensional connectivity data into a vectorial representation which is useful for classification and determining regions of brain graphs responsible for this segregation. We also propose an effective way to analyze the dynamical functional connectivity, building a similarity representation of fMRI dynamic functional connectivity states, exploiting modular properties of graph laplacians, geodesic clustering, and manifold learning
Diffusion-adapted spatial filtering of fMRI data for improved activation mapping in white matter
Brain activation mapping using fMRI data has been mostly focused on finding detections in gray matter. Activations in white matter are harder to detect due to anatomical differences between both tissue types, which are rarely acknowledged in experimental design. However, recent publications have started to show evidence for the possibility of detecting meaningful activations in white matter. The shape of the activations arising from the BOLD signal is fundamentally different between white matter and gray matter, a fact which is not taken into account when applying isotropic Gaussian filtering in the preprocessing of fMRI data. We explore a graph-based description of the white matter developed from diffusion MRI data, which is capable of encoding the anisotropic domain. Based on this representation, two approaches to white matter filtering are tested, and their performance is evaluated on both semi-synthetic phantoms and real fMRI data. The first approach relies on heat kernel filtering in the graph spectral domain, and produced a clear increase in both sensitivity and specificity over isotropic Gaussian filtering. The second approach is based on spectral decomposition for the denosing of the signal, and showed increased specificity at the cost of a lower sensitivity.Novel approach to white matter filtering We introduced new advanced methods for filtering brain scans. Using them, we managed to improve the detection of activity in the white matter of the brain
Interpretable statistics for complex modelling: quantile and topological learning
As the complexity of our data increased exponentially in the last decades, so has our
need for interpretable features. This thesis revolves around two paradigms to approach
this quest for insights.
In the first part we focus on parametric models, where the problem of interpretability
can be seen as a “parametrization selection”. We introduce a quantile-centric
parametrization and we show the advantages of our proposal in the context of regression,
where it allows to bridge the gap between classical generalized linear (mixed)
models and increasingly popular quantile methods.
The second part of the thesis, concerned with topological learning, tackles the
problem from a non-parametric perspective. As topology can be thought of as a way
of characterizing data in terms of their connectivity structure, it allows to represent
complex and possibly high dimensional through few features, such as the number of
connected components, loops and voids. We illustrate how the emerging branch of
statistics devoted to recovering topological structures in the data, Topological Data
Analysis, can be exploited both for exploratory and inferential purposes with a special
emphasis on kernels that preserve the topological information in the data.
Finally, we show with an application how these two approaches can borrow strength
from one another in the identification and description of brain activity through fMRI
data from the ABIDE project
Discovering Causal Relations and Equations from Data
Physics is a field of science that has traditionally used the scientific
method to answer questions about why natural phenomena occur and to make
testable models that explain the phenomena. Discovering equations, laws and
principles that are invariant, robust and causal explanations of the world has
been fundamental in physical sciences throughout the centuries. Discoveries
emerge from observing the world and, when possible, performing interventional
studies in the system under study. With the advent of big data and the use of
data-driven methods, causal and equation discovery fields have grown and made
progress in computer science, physics, statistics, philosophy, and many applied
fields. All these domains are intertwined and can be used to discover causal
relations, physical laws, and equations from observational data. This paper
reviews the concepts, methods, and relevant works on causal and equation
discovery in the broad field of Physics and outlines the most important
challenges and promising future lines of research. We also provide a taxonomy
for observational causal and equation discovery, point out connections, and
showcase a complete set of case studies in Earth and climate sciences, fluid
dynamics and mechanics, and the neurosciences. This review demonstrates that
discovering fundamental laws and causal relations by observing natural
phenomena is being revolutionised with the efficient exploitation of
observational data, modern machine learning algorithms and the interaction with
domain knowledge. Exciting times are ahead with many challenges and
opportunities to improve our understanding of complex systems.Comment: 137 page
A Survey on Deep Learning in Medical Image Analysis
Deep learning algorithms, in particular convolutional networks, have rapidly
become a methodology of choice for analyzing medical images. This paper reviews
the major deep learning concepts pertinent to medical image analysis and
summarizes over 300 contributions to the field, most of which appeared in the
last year. We survey the use of deep learning for image classification, object
detection, segmentation, registration, and other tasks and provide concise
overviews of studies per application area. Open challenges and directions for
future research are discussed.Comment: Revised survey includes expanded discussion section and reworked
introductory section on common deep architectures. Added missed papers from
before Feb 1st 201
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